We extensively use mice deficient for immune or inflammation-related genes and it is always difficult to distinguish a direct effect of those genes on the colitis or cancer, or an indirect one through the regulation of the intestinal microbiota. Overall these studies will greatly benefit by the access to a germ free facility that we are contributed to establish in Frederick and particularly by the availability of committed expertise in gut microbiology based on state of the art sequencing and bioinformatics, expertise that is provided by the microbiome core that we have established in Bethesda. We have established methods for the determination of mouse microbioma using 454 sequencing or MiSeq sequencingof 16 RNA, metagenomic analysis using NextSeq sequencing, and cytofluorimetric analysis of FISH labeling of specific bacterial types. We also initiated studies with germ free mice, gnotobiotic mice with defined intestinal flora, and mice reconstitute after antibiotic treatment. Initially we studied the role of the intestinal microbiota in experimental models of colitis and colitis-associated cancer using mice genetically deficient for inflammation-controlling genes such as MyD88, IL-18, TNF, TLRs, and others. In these mice the genetic defects induce a dysbiosis that can be transferred to normal mice by co-housing or fecal transplant and enhance susceptibility to chemical carcinogenesis. The bacterial species responsible of this increased susceptibility to carcinogenesis and their mechanism of action are being investigated. The role of commensal microbiota in energetic alteration associated with cancer (i.e. obesity, cachexia, anorexia, cancer treatment, irradiation) has been initiated in murine experimental models and in observational clinical experimentation. Compartmentalized control of skin immunity by resident commensals (Science. 2012;337:1115-9). Intestinal commensal bacteria induce protective and regulatory responses that maintain host-microbial mutualism. However, the contribution of tissue-resident commensals to immunity and inflammation at other barrier sites has not been addressed. We found that in mice, the skin microbiota has an autonomous role in controlling the local inflammatory milieu and tuning resident T lymphocyte function. Protective immunity to a cutaneous pathogen was found to be critically dependent on the skin microbiota but not the gut microbiota. Furthermore, skin commensals tuned the function of local T cells in a manner dependent on signaling downstream of the interleukin-1 receptor. These findings underscore the importance of the microbiota as a distinctive feature of tissue compartmentalization, and provide insight into mechanisms of immune system regulation by resident commensal niches in health and disease. Commensal bacteria control cancer response to therapy by modulating the tumor microenvironment (Science 342:967-970). The gut microbiome influences both local and systemic inflammation. Although the role of inflammation in cancer is well documented, whether commensal bacteria can exert distant effects on the inflammation in the sterile tumor microenvironment remains unclear. Here we show that microbiota perturbation impairs the response of subcutaneous cancers to CpG-oligonucleotide-immunotherapy or platinum chemotherapy. In antibiotic-treated or germ-free mice, decreased cytokine production from tumor-infiltrating monocyte-derived cells following CpG-ODN treatment reduced tumor necrosis, whereas deficient chemotherapy-induced production of reactive oxygen species by myeloid cells impaired genotoxicity and tumor destruction. Thus, optimal response to cancer immunotherapy and chemotherapy requires an intact commensal microbiota that acts distantly by modulating myeloid-derived cell function in the tumor microenvironment. These findings underscore the importance of the microbiota in the outcome of disease treatment. The toxicity mediated by cisplatin (intestinal mucosa damage, nephrotoxicity, decrease of adipose and muscular tissues (cachexia)) require the presence of gut microbiota. The participation of different microbial species and the mechanisms by which they allow the cisplatin toxicity are being investigated. We also study cancer associated cachexia in mice and humans to investigate whether the microbiota regulates the establishment of this devastating cancer comorbidity and could be targeted therapeutically. In mice we focused initially on a model of cachexia induced by the Lewis Lung Carcinoma (LLC) tumor that in 18-21 days induces weight loss associated with loss of adipose and muscle tissue. LLC-induced cachexia is due to increased lipolysis in the white adipose tissue (WAT). Unlike what we observed in cisplatin induced cachexia, beiging (switch from WAT to brown adipose tissue) is not an important component of LLC induced cachexia. LLC induces cachexia by inducing WAT infiltration of c-Kit expressing immature oxidative neutrophils that induce lipolysis by ROS production. Deletion of neutrophils or treatment of mice with N-acetyl cysteine prevent cachexia. Cachexia is accelerated in germ free mice due to increased lipolysis and failure to upregulate compensatory mechanisms, adipogenesis and lipogenesis. The microbiota delays cancer cachexia at least in part by producing SCFA that regulate lipolysis, lipogenesis and adipogenesis. The results obtained in the LLC model showing absence of beiging, neutrophil infiltration and lack of dependence from IL-6 differ in part from those described in other experimental models. Because different tumor types may induce cachexia through different mechanisms in mice as well as in patients, we will compare the mechanism involved and the role of the microbiota in different models (SW480, 4T1 and C26 transplantable tumors; Kras/P53 pancreatic GEMM and cell lines). Kras/P53 mice and cell lines will be studied in collaboration with Perwez Hussein, CCR. The group of Dan McVicar, CIP, has shown in the spleen of 4T1 tumor bearing animals that immature neutrophils, defined by expression of c-Kit and dependent on c-Kit signaling, possess the capacity for oxidative mitochondrial metabolism and in limited glucose use their mitochondria to support NADPH-oxidase dependent ROS production via fatty acid oxidation. The characteristics of these splenic neutrophils are like those that we observed in the cachectic adipose tissue and that induce lipolysis through ROS, thus we plan to collaborate with Dan McVicar in studying the metabolism of neutrophil and adipose tissue during cachexia. The role of the microbiota will be studied by modifying the microbiota by diet (e.g. diet supplemented with soluble fibers such as inulin) or other perturbations (followed by metagenomic and metatranscriptomic analysis) or by targeted gnotobiotic experiments, focusing initially on the production of SCFA. Cancer patients' neutrophils display immaturity and oxidative metabolism, thus, the mechanism of cachexia observed in mice may extend to humans. We collaborate with Marilia Seelaender, University of Sao Paulo, testing the hypothesis that in cachectic patients gut barrier disruption associated with altered microbiota composition may elicit persistent immune activation in the host. We have analyzed 7 cachectic patients with colorectal cancer (CC) and 14 weight stable patients (WSC) by 16S analysis. We will extend this analysis to a larger number of patients by metagenomic and metatranscriptomic analysis. The initial studies have shown an increased number of lymphoid aggregates in CC patients associated with degradation of mucus layer, infiltration with eosinophils, increased G-CSF, IL-13 and TGF-beta thus showing analogy with the mouse results.